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Merge branch 'releases/Release_2_10_4_Branch' into develop
[jalview.git] / src /
2018-01-26 kiramtJAL-2778 tightened up use of resetAlignmentDims tree | commitdiff
2018-01-25 kiramtJAL-2778 Tidy tree | commitdiff
2018-01-25 kiramtJAL-2778 added JAL-2851 fix to avoid confusion tree | commitdiff
2018-01-25 kiramtJAL-2778 Reinstate id width adjuster tree | commitdiff
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence... tree | commitdiff
2018-01-22 kiramtJAL-2759 Various minor HiddenColumns updates after... tree | commitdiff
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after... tree | commitdiff
2018-01-19 kiramtJAL-2759 Moved propagateInsertions out of HiddenColumns tree | commitdiff
2018-01-19 kiramtJAL-2759 Update to getVisibleStartAndEndIndex after... tree | commitdiff
2018-01-18 kiramtJAL-2759 change subtractVisibleColumns and removal... tree | commitdiff
2018-01-18 gmungocJAL-2810 JAL-2886 i18n tree | commitdiff
2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved... tree | commitdiff
2018-01-18 kiramtJAL-2759 Updated test tree | commitdiff
2018-01-18 kiramtJAL-2759 unit tests (incomplete) tree | commitdiff
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri... tree | commitdiff
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren... tree | commitdiff
2018-01-16 kiramtJAL-2759 setup hideBitSet over range for hideInsertions tree | commitdiff
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam... tree | commitdiff
2018-01-16 gmungocJAL-1270 JAL-2885 clear properties before load tree | commitdiff
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC... tree | commitdiff
2018-01-16 kiramtJAL-2759 Replaced StringBuffer with StringBuilder;... tree | commitdiff
2018-01-15 kiramtJAL-2759 More compact iterator usage; after review tree | commitdiff
2018-01-15 kiramtJAL-2759 First pass instantiate hiddenColumns collectio... tree | commitdiff
2018-01-15 kiramtJAL-2759 getVisContigsIterator returns VisibleContigsIt... tree | commitdiff
2018-01-15 kiramtJAL-2759 Rename hideInsertionsFor to hideList, after... tree | commitdiff
2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review tree | commitdiff
2018-01-15 kiramtJAL-2759 Simplified HiddenColumns constructor after... tree | commitdiff
2018-01-15 kiramtJAL-2759 Changed VisibleColsCollection constructor... tree | commitdiff
2018-01-15 kiramtJAL-2759 Minor doc and naming changes tree | commitdiff
2018-01-15 kiramtJAL-2759 Updated absoluteToVisibleColumn doc (prev... tree | commitdiff
2018-01-15 kiramtJAL-2759 Rename findColumnPosition and adjustForHiddenC... tree | commitdiff
2018-01-15 kiramtJAL-2759 Renamed BoundedHiddenColsIterator to HiddenCol... tree | commitdiff
2018-01-15 kiramtJAL-2759 Comments and renaming for has(Many)HiddenColum... tree | commitdiff
2018-01-15 kiramtJAL-2759 Tidy up javadoc and naming in HiddenColumnsCur... tree | commitdiff
2018-01-15 kiramtJAL-2759 Update to getHiddenBoundaryRight + unit test... tree | commitdiff
2018-01-15 kiramtJAL-2759 Updates following review tree | commitdiff
2018-01-10 gmungocJAL-1793 update spike branch to latest tree | commitdiff
2018-01-10 gmungocJAL-2791 ignore feature type visibility in getColor() tree | commitdiff
2018-01-09 gmungocJAL-2843 unit tests for Save/Load colours and filters... tree | commitdiff
2018-01-09 gmungocJAL-2808 small tweaks to api / Javadoc tree | commitdiff
2018-01-08 gmungocJAL-2069 fix setting initial value of slider from threshold tree | commitdiff
2017-12-14 gmungocJAL-2843 missed Castor class tree | commitdiff
2017-12-14 gmungocJAL-2843 save/restore colour feature by attribute,... tree | commitdiff
2017-12-14 gmungocJAL-2879 save/restore feature sub-attributes in Jalview... tree | commitdiff
2017-12-14 gmungocJAL-2843 missed Castor class tree | commitdiff
2017-12-14 gmungocJAL-2843 and Castor metadata file for latest changes tree | commitdiff
2017-12-14 gmungocJAL-2843 schema and code changes to save colour by... tree | commitdiff
2017-12-13 gmungocJAL-2843 add isByAttribute to interface for convenience tree | commitdiff
2017-12-11 gmungocJAL-2843 add colour by attribute, and no value colour... tree | commitdiff
2017-12-08 gmungocJAL-2843 read/write feature filters from/to Jalview... tree | commitdiff
2017-12-08 gmungocJAL-2843 refactor / tidy for feature filter input/output tree | commitdiff
2017-12-08 gmungocJAL-2843 methods relocated tree | commitdiff
2017-12-08 gmungocJAL-2843 toStableString, fromString for Jalview feature... tree | commitdiff
2017-12-08 gmungocJAL-2843 FeatureRenderer.getFeatureFilters returns... tree | commitdiff
2017-12-05 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-12-04 gmungocJAL-2808 JAL-2850 update spike build to latest tree | commitdiff
2017-12-04 gmungocMerge branch 'spikes/mungo' into features/JAL-1793VCF tree | commitdiff
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere... tree | commitdiff
2017-12-04 gmungocJAL-2845 locate reverse strand insertion as complement... tree | commitdiff
2017-12-04 gmungocJAL-2835 small refactor to only extract transcript... tree | commitdiff
2017-12-01 gmungocJAL-2835 spike updated to latest (use specific SO term... tree | commitdiff
2017-12-01 gmungocJAL-2835 refactored to extract specific consequence... tree | commitdiff
2017-12-01 gmungocJAL-2792 sort feature attributes for output, not for... tree | commitdiff
2017-12-01 gmungocJAL-2835 additional sub-terms of sequence_variant added tree | commitdiff
2017-11-30 gmungocJAL-2850 improved use of htsjdk api to read contig... tree | commitdiff
2017-11-30 gmungocJAL-1766 additional tests for stub htsjdk wrapper tree | commitdiff
2017-11-30 Jim ProcterJAL-2849 JAL-2863 file format preferences TODO
 tree | commitdiff
2017-11-30 Jim ProcterJAL-2849 fix tree | commitdiff
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2859_uniprottowrongpdbid' into... tree | commitdiff
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2740' into develop tree | commitdiff
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2827' into develop tree | commitdiff
2017-11-28 Jim ProcterMerge branch 'bug/JAL-2842' into develop tree | commitdiff
2017-11-28 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-11-28 gmungocJAL-2850 MapList.isToForwardStrand added tree | commitdiff
2017-11-27 Jim ProcterJAL-2859 disambiguate with PDB ID if no file path bug/JAL-2859_uniprottowrongpdbid tree | commitdiff
2017-11-27 gmungocJAL-2850 VCFLoader refactored to load VCF to contig... tree | commitdiff
2017-11-24 gmungocJAL-2808 update spike to latest tree | commitdiff
2017-11-24 gmungocJAL-2808 refactoring to better handler filter by Score... tree | commitdiff
2017-11-24 gmungocJAL-2808 relocate constants for compiler, add COLUMN_CO... tree | commitdiff
2017-11-24 gmungocJAL-2808 refine FeatureMatcher interface and matcher... tree | commitdiff
2017-11-24 gmungocJAL-2808 don't cache i18n - MessageManager already... tree | commitdiff
2017-11-23 gmungocJAL-2808 update spike to latest (filter range tooltip... tree | commitdiff
2017-11-23 gmungocJAL-2808 refactor KeyedMatcher as FeatureMatcher with... tree | commitdiff
2017-11-23 gmungocJAL-2808 update spike to latest (filter range, Present... tree | commitdiff
2017-11-23 gmungocJAL-2808 removed field filters; sort CSQ data by key tree | commitdiff
2017-11-23 gmungocJAL-2808 added conditions Present, NotPresent as options tree | commitdiff
2017-11-23 kiramtMerge branch 'develop' into bug/JAL-2851 bug/JAL-2851 tree | commitdiff
2017-11-23 kiramtJAL-2851 Fix merge error breaking vertical scrolling tree | commitdiff
2017-11-23 gmungocJAL-2808 refactor conversion of table data to beans... tree | commitdiff
2017-11-23 gmungocJAL-2808 pass FeatureSettings to controller as array... tree | commitdiff
2017-11-22 gmungocJAL-2808 update conditions list on change of attribute... tree | commitdiff
2017-11-22 kiramtJAL-2842 JAL-2759 change to SeqPanel moveCursor tree | commitdiff
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) tree | commitdiff
2017-11-22 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-11-22 gmungocJAL-2808 JAL-2069 FeatureTypeSettings (with new Filters... tree | commitdiff
2017-11-22 kiramtJAL-2759 code tidy tree | commitdiff
2017-11-22 kiramtJAL-2759 performance improvements to hideColumns tree | commitdiff
2017-11-22 gmungocJAL-2069 renamed helper method better tree | commitdiff
2017-11-22 gmungocJAL-2808 defer dispose to allow screen location to... tree | commitdiff
2017-11-22 gmungocJAL-2069 Javadoc added only tree | commitdiff
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